Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.

ABSTRACT: Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)-based studies have revealed little sequence difference, with 0.1%-0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference genome and ignored the contribution of larger-scale structural variants (SVs). We constructed a pangenome graph that integrates six new and two existing long-read genome assemblies of Lake Malawi haplochromine cichlids. This grap

SUBMITTER: Quah FX 

PROVIDER: S-EPMC12047535 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature